Herein, we report the rational fabrication of unique core–shell nanoclusters composed of cobalt carbonate hydroxide (Co-CH) @ nickel aluminum layered double hydroxide (NiAl-LDH) on a carbon cloth (CC) substrate using a two-step hydrothermal strategy. The one-dimensional (1D) Co-CH nanowires core–shell functions as a framework for the growth of two-dimensional (2D) NiAl-LDH nanosheets, leading to the formation of a hierarchically porous core–shell heterostructure. The presence of abundant heterointerfaces enhances electrical conductivity, reduces charge transfer resistance, and facilitates ion/electron transfer. Taking full advantage of its unique nanostructure and synergistic effect of two components, the as-prepared Co-CH@NiAl-LDH hybrid material illustrates a specific capacity of 1029.4 C/g (2058.9 mC cm−2) at 1 A g−1 and good rate capability with a capacity retention of 68.5% at 20 A g−1. Additionally, the assembled Co-CH@NiAl-LDH//pine pollen-derived porous carbon (PPC) hybrid supercapacitor (HSC) delivers impressive energy and power densities of 66.2 Wh kg−1 (0.27 Wh cm−2) and 17529.7 Wh kg−1 (0.11 Wh cm−2), respectively. This device also achieves a superior capacity retention of 80.3% over 20,000 cycles. These findings prove the importance of engineering heterointerfaces in heterostructure for the promotion of energy storage performance.